Research workbench
Structure of human DNA polymerase iota bound to template 1-methyl- deoxyadenosine
Analyse Structure of human DNA polymerase iota bound to template 1-methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ULW
- Type
- protein + DNA
- Length
- 389 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'); DNA (5'-D(*TP*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3')…
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- TTP, MG, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3') | dna | 7 | — | — |
| T | DNA (5'-D(*TP*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3') | dna | 9 | — | — |
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 373 | 47% helix, 20% strand | Q9UNA4 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains P, T, A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.77 | 0.80 | 69 | TTP |
| 2 | 741 | 0.74 | 0.79 | 53 | empty |
| 3 | 80 | 0.52 | 0.84 | 14 | empty |
| 4 | 79 | 0.32 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- T–A · 734 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–A · 456 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 332 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ULW · Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine · the same entry in another collection · chain P against P, TM-score 1.00
- Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9UNA4
- Elsewhere: RCSB PDB 5ULW · PDBe 5ULW · UniProt Q9UNA4
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